There are two basic options for installing
msprime: either through
pre-built binary packages using conda or
by compiling locally using pip. We recommend using
for most users, although
pip can be more convenient in certain cases.
If you installed Python using anaconda/miniconda, please install
conda. Link/load time errors will occur if you mix
a conda installed Python with system libraries.
condausing miniconda. Make sure you follow the instructions to fully activate your
- Set up the conda-forge channel using
conda config --add channels conda-forge.
- Install msprime:
conda install msprime.
- Try it out:
There are several different ways to obtain
conda. Please see the
anaconda installation documentation
for full details.
In this example we create a
msprime into it on an OSX machine.
We assume that
conda has been installed and bash shell is being used (Windows users will need to modify the
$ conda create --name msprime-env Solving environment: done ## Package Plan ## environment location: /Users/jk/miniconda3/envs/msprime-env Proceed ([y]/n)? y Preparing transaction: done Verifying transaction: done Executing transaction: done # # To activate this environment, use # # $ conda activate msprime-env # # To deactivate an active environment, use # # $ conda deactivate $ source activate msprime-env (msprime-env) $ conda install -c conda-forge msprime Solving environment: done ## Package Plan ## environment location: /Users/jk/miniconda3/envs/msprime-env added / updated specs: - msprime The following NEW packages will be INSTALLED: ca-certificates: 2018.1.18-0 conda-forge certifi: 2018.1.18-py36_0 conda-forge gsl: 1.16-0 conda-forge hdf5: 1.10.1-2 conda-forge intel-openmp: 2018.0.0-h8158457_8 libgfortran: 3.0.1-h93005f0_2 mkl: 2018.0.1-hfbd8650_4 msprime: 0.5.0b2-py36_3 conda-forge ncurses: 5.9-10 conda-forge numpy: 1.14.1-py36h8a80b8c_1 openssl: 1.0.2n-0 conda-forge pip: 9.0.1-py36_1 conda-forge pyparsing: 2.2.0-py36_0 conda-forge python: 3.6.4-0 conda-forge readline: 7.0-0 conda-forge setuptools: 38.5.1-py36_0 conda-forge six: 1.11.0-py36_1 conda-forge sqlite: 3.20.1-2 conda-forge svgwrite: 1.1.12-py_0 conda-forge tk: 8.6.7-0 conda-forge wheel: 0.30.0-py36_2 conda-forge xz: 5.2.3-0 conda-forge zlib: 1.2.11-0 conda-forge Proceed ([y]/n)? y Preparing transaction: done Verifying transaction: done Executing transaction: done (msprime-env) $ python Python 3.6.4 | packaged by conda-forge | (default, Dec 23 2017, 16:54:01) [GCC 4.2.1 Compatible Apple LLVM 6.1.0 (clang-602.0.53)] on darwin Type "help", "copyright", "credits" or "license" for more information. >>> import msprime >>> tree = msprime.simulate(5).first() >>> print(tree.draw(format="unicode")) 8 ┏━┻━━┓ ┃ 7 ┃ ┏━┻━┓ ┃ ┃ 6 ┃ ┃ ┏┻┓ ┃ 5 ┃ ┃ ┃ ┏┻┓ ┃ ┃ 1 0 4 2 3
Please see the conda documentation for more details on managing packages and environments.
pip is more flexible than
conda as it
can support more versions of Python, and the locations of the
various dependencies can be specified.
pip is the recommended method when using the
system provided Python installations.
Installing system requirements¶
When installing via
pip, GSL must be installed using system packages
(we do not recommend installing GSL from source). GSL packages are available
on all major platforms.
For example, to install on Debian/Ubuntu use (as root):
$ apt-get install python-dev libgsl0-dev
For Redhat/Fedora use:
$ yum install gsl-devel
On FreeBSD we can use
pkg to install the requirements:
$ pkg install gsl
To install the dependencies on OS X, we can use Homebrew:
$ brew update $ brew install gsl
We can install
msprime easily using pip:
$ python3 -m pip install msprime
(It is generally better to use
python3 -m pip rather than call
directly since this allows you to control which installation of Python the
package is installed to.) This will work in most cases, once the GSL has been
installed. See below for platform specific build instructions when this fails.
If you do not have root access to your machine, you can install
msprime into your local Python installation as follows:
$ python3 -m pip install msprime --user
To use the
mspms program you must ensure
~/.local/bin directory is in your
simply run it using:
msprime, simply run:
$ python3 -m pip uninstall msprime
Platform specific installation¶
This section contains instructions to build on platforms that require build time flags for GSL.
To install and run
msprime on a fresh Ubuntu 15.10 installation, do the
$ sudo apt-get install pkg-config python-dev python-pip libgsl0-dev $ pip install msprime --user $ ~/.local/bin/mspms 2 1 -t 1 /usr/local/bin/mspms 2 1 -t 1 5338 8035 23205 // segsites: 3 positions: 0.014 0.045 0.573 100 011
Install the prerequisitites, and build
msprime as follows:
$ pkg install gsl $ CFLAGS=-I/usr/local/include LDFLAGS=-L/usr/local/lib pip install msprime
This assumes that root is logged in using a bash shell. For other shells,
different methods are need to set the
OS X Homebrew¶
We recommend using conda to install
msprime on OS X.
However, it is also possible to install using Homebrew to satisfy the
First, ensure that Homebrew is installed and up-to-date:
$ brew update
We need to ensure that the version of Python we used is installed via Homebrew (there can be linking issues if we use the built-in version of Python or a version from Anaconda). Therefore, we install Python 3 using homebrew:
$ brew install python3 $ pip3 install --upgrade pip setuptools
The previous step can be skipped if you wish to use your own Python installation, and already have a working pip.
Now install the dependencies and msprime:
$ brew install gsl $ pip3 install msprime
Check if it works:
$ mspms 10 1 -T
Python 2 users¶
Msprime no longer supports Python 2, and therefore those wishing to continue using Python 2.7 will not be able to take advantage of newer features. We recommend using msprime version 0.6.2 if you need to work with Python 2.7:
$ python -m pip install msprime==0.6.2
$ conda install msprime==0.6.2